The cumulative coalescent function (CCF) describes the fraction a given target genome shares with a comparator genome due to common ancestry; the curve is monotonically increasing back in time. The CCF was inferred using a dynamic programming method which takes the alleles carried by the target genome, compares those to the alleles carried by the comparator genome, and infers the CCF based on the estimated age of the shared alleles. Here, allele age estimated using the joint clock model was applied throughout.

CIF

The coalescent intensity function (CIF) corresponds to the rate of change of coalescence (i.e. common ancestry) during a given time interval ("epoch"). The CIF is computed from the CCF between the target and a comparator individual. Here, CIFs were scaled across the sample per epoch (columns), such that the maximum value is equal to 1 per epoch.

Aggregation

The CCF is inferred between two haploid genomes (i.e. phased chromosomes). To summarise the ancestry shared between diploid individuals, the CCFs between each of the two target genomes and the two comparator genomes are "aggregated" by computing the weighted mean across individual chromosomes (weighted by the number of dated variants per chromosome) and averaged per individual.

Relatedness ranking

An approximate measure of relatedness within the sample is provided by computing the area under the curve (AUC) of the CCFs inferred between target and comparator individuals (after aggregation). The ranking is obtained by sorting comparator individuals from highest to lowest AUC. The AUC was computed on log-scaled time, thereby giving higher importance to more recently shared ancestry.